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1RFU
Asym. Unit
Info
Asym.Unit (413 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (107 KB)
Biol.Unit 3 (106 KB)
Biol.Unit 4 (106 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PYRIDOXAL KINASE COMPLEXED WITH ADP AND PLP
Authors
:
D. -C. Liang, T. Jiang, M. -H. Li
Date
:
10 Nov 03 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,H (1x)
Biol. Unit 4: D,G (1x)
Keywords
:
Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. -H. Li, F. Kwok, W. -R. Chang, S. -Q. Liu, S. C. L. Lo, J. -P. Zhang, T. Jiang, D. -C. Liang
Conformational Changes In The Reaction Of Pyridoxal Kinase
J. Biol. Chem. V. 279 17459 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 24)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
2e: PYRIDOXAL-5'-PHOSPHATE (PLPe)
2f: PYRIDOXAL-5'-PHOSPHATE (PLPf)
2g: PYRIDOXAL-5'-PHOSPHATE (PLPg)
2h: PYRIDOXAL-5'-PHOSPHATE (PLPh)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
8
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
PLP
8
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
3
ZN
8
Ligand/Ion
ZINC ION
[
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]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:127 , PLP A:401 , ADP A:402
BINDING SITE FOR RESIDUE ZN A 403
02
AC2
SOFTWARE
VAL B:115 , PLP B:1401 , ADP B:1402
BINDING SITE FOR RESIDUE ZN B 1403
03
AC3
SOFTWARE
VAL C:115 , PLP C:2401 , ADP C:2402
BINDING SITE FOR RESIDUE ZN C 2403
04
AC4
SOFTWARE
ASP D:113 , VAL D:115 , PLP D:3401 , ADP D:3402
BINDING SITE FOR RESIDUE ZN D 3403
05
AC5
SOFTWARE
ASP E:113 , VAL E:115 , PLP E:4401 , ADP E:4402
BINDING SITE FOR RESIDUE ZN E 4403
06
AC6
SOFTWARE
ASP F:113 , VAL F:115 , PLP F:5401 , ADP F:5402
BINDING SITE FOR RESIDUE ZN F 5403
07
AC7
SOFTWARE
ASP G:113 , PLP G:6401 , ADP G:6402
BINDING SITE FOR RESIDUE ZN G 6403
08
AC8
SOFTWARE
ASP H:113 , VAL H:115 , PLP H:7401 , ADP H:7402
BINDING SITE FOR RESIDUE ZN H 7403
09
AC9
SOFTWARE
SER A:12 , VAL A:19 , THR A:47 , TYR A:84 , TYR A:127 , VAL A:231 , GLY A:232 , THR A:233 , GLY A:234 , ASP A:235 , ADP A:402 , ZN A:403
BINDING SITE FOR RESIDUE PLP A 401
10
BC1
SOFTWARE
ASN A:150 , THR A:186 , SER A:187 , LEU A:199 , MET A:223 , HIS A:224 , LYS A:225 , VAL A:226 , ALA A:228 , THR A:233 , GLY A:234 , PHE A:237 , MET A:263 , LEU A:267 , PLP A:401 , ZN A:403
BINDING SITE FOR RESIDUE ADP A 402
11
BC2
SOFTWARE
SER B:12 , VAL B:19 , THR B:47 , TYR B:84 , TYR B:127 , VAL B:231 , GLY B:232 , THR B:233 , GLY B:234 , ASP B:235 , ADP B:1402 , ZN B:1403
BINDING SITE FOR RESIDUE PLP B 1401
12
BC3
SOFTWARE
THR B:186 , SER B:187 , MET B:223 , HIS B:224 , LYS B:225 , VAL B:226 , ALA B:228 , THR B:233 , GLY B:234 , MET B:263 , LEU B:267 , PLP B:1401 , ZN B:1403
BINDING SITE FOR RESIDUE ADP B 1402
13
BC4
SOFTWARE
SER C:12 , VAL C:19 , THR C:47 , TYR C:84 , TYR C:127 , VAL C:231 , GLY C:232 , THR C:233 , GLY C:234 , ASP C:235 , ADP C:2402 , ZN C:2403
BINDING SITE FOR RESIDUE PLP C 2401
14
BC5
SOFTWARE
ASN C:150 , THR C:186 , SER C:187 , LEU C:199 , MET C:223 , HIS C:224 , LYS C:225 , VAL C:226 , ALA C:228 , THR C:233 , GLY C:234 , MET C:263 , LEU C:267 , PLP C:2401 , ZN C:2403
BINDING SITE FOR RESIDUE ADP C 2402
15
BC6
SOFTWARE
SER D:12 , VAL D:19 , THR D:47 , TYR D:84 , TYR D:127 , VAL D:231 , GLY D:232 , THR D:233 , GLY D:234 , ASP D:235 , ADP D:3402 , ZN D:3403
BINDING SITE FOR RESIDUE PLP D 3401
16
BC7
SOFTWARE
ASN D:150 , THR D:186 , SER D:187 , LEU D:199 , MET D:223 , HIS D:224 , LYS D:225 , VAL D:226 , ALA D:228 , THR D:233 , GLY D:234 , MET D:263 , LEU D:267 , PLP D:3401 , ZN D:3403
BINDING SITE FOR RESIDUE ADP D 3402
17
BC8
SOFTWARE
SER E:12 , VAL E:19 , THR E:47 , TYR E:84 , TYR E:127 , VAL E:231 , GLY E:232 , THR E:233 , GLY E:234 , ASP E:235 , ADP E:4402 , ZN E:4403
BINDING SITE FOR RESIDUE PLP E 4401
18
BC9
SOFTWARE
ASN E:150 , THR E:186 , SER E:187 , MET E:223 , HIS E:224 , LYS E:225 , VAL E:226 , ALA E:228 , THR E:233 , GLY E:234 , MET E:263 , LEU E:267 , PLP E:4401 , ZN E:4403
BINDING SITE FOR RESIDUE ADP E 4402
19
CC1
SOFTWARE
SER F:12 , VAL F:19 , THR F:47 , TYR F:84 , TYR F:127 , VAL F:231 , GLY F:232 , GLY F:234 , ASP F:235 , ADP F:5402 , ZN F:5403
BINDING SITE FOR RESIDUE PLP F 5401
20
CC2
SOFTWARE
ASN F:150 , THR F:186 , SER F:187 , MET F:223 , HIS F:224 , LYS F:225 , VAL F:226 , ALA F:228 , THR F:233 , GLY F:234 , MET F:263 , LEU F:267 , PLP F:5401 , ZN F:5403
BINDING SITE FOR RESIDUE ADP F 5402
21
CC3
SOFTWARE
SER G:12 , VAL G:19 , THR G:47 , TYR G:84 , TYR G:127 , VAL G:231 , GLY G:232 , GLY G:234 , ASP G:235 , ADP G:6402 , ZN G:6403
BINDING SITE FOR RESIDUE PLP G 6401
22
CC4
SOFTWARE
ASN G:150 , THR G:186 , SER G:187 , MET G:223 , HIS G:224 , LYS G:225 , VAL G:226 , ALA G:228 , THR G:233 , GLY G:234 , MET G:263 , LEU G:267 , PLP G:6401 , ZN G:6403
BINDING SITE FOR RESIDUE ADP G 6402
23
CC5
SOFTWARE
SER H:12 , VAL H:19 , THR H:47 , TYR H:84 , TYR H:127 , VAL H:231 , GLY H:232 , THR H:233 , GLY H:234 , ASP H:235 , ADP H:7402 , ZN H:7403
BINDING SITE FOR RESIDUE PLP H 7401
24
CC6
SOFTWARE
ASN H:150 , THR H:186 , SER H:187 , MET H:223 , HIS H:224 , LYS H:225 , VAL H:226 , ALA H:228 , THR H:233 , GLY H:234 , MET H:263 , LEU H:267 , PLP H:7401 , ZN H:7403
BINDING SITE FOR RESIDUE ADP H 7402
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1rfua_ (A:)
1b: SCOP_d1rfub_ (B:)
1c: SCOP_d1rfuc_ (C:)
1d: SCOP_d1rfud_ (D:)
1e: SCOP_d1rfue_ (E:)
1f: SCOP_d1rfuf_ (F:)
1g: SCOP_d1rfug_ (G:)
1h: SCOP_d1rfuh_ (H:)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
PfkB-like kinase
(20)
Protein domain
:
Pyridoxal kinase
(8)
Sheep (Ovis aries) [TaxId: 9940]
(8)
1a
d1rfua_
A:
1b
d1rfub_
B:
1c
d1rfuc_
C:
1d
d1rfud_
D:
1e
d1rfue_
E:
1f
d1rfuf_
F:
1g
d1rfug_
G:
1h
d1rfuh_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1rfuA00 (A:1-312)
1b: CATH_1rfuB00 (B:1-312)
1c: CATH_1rfuC00 (C:1-312)
1d: CATH_1rfuD00 (D:1-312)
1e: CATH_1rfuE00 (E:1-312)
1f: CATH_1rfuF00 (F:1-312)
1g: CATH_1rfuG00 (G:1-312)
1h: CATH_1rfuH00 (H:1-312)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.20, no name defined]
(73)
Sheep (Ovis aries)
(8)
1a
1rfuA00
A:1-312
1b
1rfuB00
B:1-312
1c
1rfuC00
C:1-312
1d
1rfuD00
D:1-312
1e
1rfuE00
E:1-312
1f
1rfuF00
F:1-312
1g
1rfuG00
G:1-312
1h
1rfuH00
H:1-312
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_PfkB_1rfuH01 (H:2-284)
1b: PFAM_PfkB_1rfuH02 (H:2-284)
1c: PFAM_PfkB_1rfuH03 (H:2-284)
1d: PFAM_PfkB_1rfuH04 (H:2-284)
1e: PFAM_PfkB_1rfuH05 (H:2-284)
1f: PFAM_PfkB_1rfuH06 (H:2-284)
1g: PFAM_PfkB_1rfuH07 (H:2-284)
1h: PFAM_PfkB_1rfuH08 (H:2-284)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ribokinase
(55)
Family
:
PfkB
(39)
Ovis aries (Sheep)
(7)
1a
PfkB-1rfuH01
H:2-284
1b
PfkB-1rfuH02
H:2-284
1c
PfkB-1rfuH03
H:2-284
1d
PfkB-1rfuH04
H:2-284
1e
PfkB-1rfuH05
H:2-284
1f
PfkB-1rfuH06
H:2-284
1g
PfkB-1rfuH07
H:2-284
1h
PfkB-1rfuH08
H:2-284
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